[Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem

hi Valerie,

regarding the bug you fixed about a month ago and described below, 
there's something still not entirely correct that i did not notice then, 
or maybe something has broken since then. Let me run the example again 
to explain it:

library(Biostrings)
library(BiocParallel)

bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character, 
BPPARAM=bpparam("SerialParam"))
[1] "AC" "GT"

## this looks fine so far but notice the result when i call
## now the function 'class()' instead of 'as.character()'

bpvec(X=DNAStringSet(c("AC", "GT")), FUN=class, 
BPPARAM=bpparam("SerialParam"))
[1] "DNAString" "DNAString"

somehow bpvec() is chopping the input into objects of a class different 
to the original input class. this does not happen with the multicore 
backend:

bpvec(X=DNAStringSet(c("AC", "GT")), FUN=class, 
BPPARAM=bpparam("MulticoreParam"))
[1] "DNAStringSet" "DNAStringSet"


so, i guess there's still something wrong with the SerialParam backend.


thanks!!

robert.


On 09/05/2015 12:10 AM, Obenchain, Valerie wrote:

Hi Robert,

Thanks for reporting the bug. The problem was with how 'X' was split
before dispatching to bplapply() and affected both SerialParam and
SnowParam. Now fixed in release (1.2.21) and devel (1.3.52).

Valerie

----- Forwarded Message -----
From: "Robert Castelo"<robert.castelo at upf.edu>
To: bioc-devel at r-project.org
Sent: Wednesday, September 2, 2015 8:12:33 AM
Subject: [Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem

hi,

I have encountered a problem when using the bpvec() function from the
BiocParallel package with DNAStringSet objects and the "SerialParam"
backend:

library(Biostrings)
library(BiocParallel)


## all correct when using the multicore backend

bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character, BPPARAM=bpparam())
[1] "AC" "GT"

bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character,
BPPARAM=MulticoreParam())
[1] "AC" "GT"


## problem when using the SerialParam backend

bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character,
BPPARAM=bpparam("SerialParam"))
[1] "1" "2"


the problem is that elements of the DNAStringSet object get somehow
coerced to integers when using the "SerialParam" backend.


this occurs in both current release and devel, please find the
corresponding sessionInfo()'s below.


thanks!

robert.

## release
sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Fedora release 12 (Constantine)

locale:
   [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
   [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
   [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
   [7] LC_PAPER=en_US.UTF8       LC_NAME=C
   [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] BiocParallel_1.2.20 Biostrings_2.36.4   XVector_0.8.0
[4] IRanges_2.2.7       S4Vectors_0.6.5     BiocGenerics_0.14.0
[7] vimcom_1.2-3        setwidth_1.0-4      colorout_1.1-0

loaded via a namespace (and not attached):
[1] zlibbioc_1.14.0      futile.logger_1.4.1  tools_3.2.0
[4] lambda.r_1.1.7       futile.options_1.0.0

## devel
sessionInfo()
R Under development (unstable) (2015-04-28 r68268)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Fedora release 12 (Constantine)

locale:
   [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
LC_TIME=en_US.UTF8
   [4] LC_COLLATE=en_US.UTF8     LC_MONETARY=en_US.UTF8
LC_MESSAGES=en_US.UTF8
   [7] LC_PAPER=en_US.UTF8       LC_NAME=C                 LC_ADDRESS=C

[10] LC_TELEPHONE=C            LC_MEASUREMENT=en_US.UTF8
LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
   methods   base

other attached packages:
[1] BiocParallel_1.3.51 Biostrings_2.37.8   XVector_0.9.3
IRanges_2.3.18
[5] S4Vectors_0.7.14    BiocGenerics_0.15.6 vimcom_1.0-0
setwidth_1.0-4
[9] colorout_1.0-3

loaded via a namespace (and not attached):
[1] zlibbioc_1.15.0      futile.logger_1.4.1  tools_3.3.0
lambda.r_1.1.7
[5] futile.options_1.0.0

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